Uses of Class
pal.coalescent.DemographicModel
Packages that use DemographicModel
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Utility classes for converting PAL objects to and from XML documents.
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Uses of DemographicModel in pal.coalescent
Subclasses of DemographicModel in pal.coalescentModifier and TypeClassDescriptionclassThis class models coalescent intervals for a constant population (parameter: N0=present-day population size).classThis class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.classThis class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.classThis class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.classThis class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).Methods in pal.coalescent that return DemographicModelModifier and TypeMethodDescriptionDemographicClockTree.getDemographicModel()Return the demographic model being used to optimize the likelihood of this tree.DemographicTree.getDemographicModel()Methods in pal.coalescent with parameters of type DemographicModelModifier and TypeMethodDescriptiondoubleCoalescentIntervals.computeLogLikelihood(DemographicModel model) Returns the log likelihood of this set of coalescent intervals, given a demographic model.CoalescentSimulator.simulateIntervals(int numLines, DemographicModel model) Simulates a set of CoalescentIntervals from a genealogy assuming contemporaneous tips.SerialCoalescentSimulator.simulateIntervals(TimeOrderCharacterData tocd, DemographicModel model, boolean createTree) Simulates a set of CoalescentIntervals from a genealogy.Constructors in pal.coalescent with parameters of type DemographicModelModifierConstructorDescriptionDemographicClockTree(Tree t, DemographicModel model) take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate) Results will not contain alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher) Results will not contain alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory) SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory) -
Uses of DemographicModel in pal.eval
Fields in pal.eval declared as DemographicModelMethods in pal.eval that return DemographicModelModifier and TypeMethodDescriptionDemographicValue.getDemographicModel()Returns the demographic model of this likelihood valueMethods in pal.eval with parameters of type DemographicModelModifier and TypeMethodDescriptionvoidDemographicValue.setDemographicModel(DemographicModel m) define model -
Uses of DemographicModel in pal.supgma
Methods in pal.supgma that return DemographicModelModifier and TypeMethodDescriptionThetaHandler.generateDemographicModel(double[] deltas, double[] thetas, TimeOrderCharacterData tocd) May return null if not possible to infer demographic model -
Uses of DemographicModel in pal.xml
Methods in pal.xml that return DemographicModelModifier and TypeMethodDescriptionstatic DemographicModelElementParser.parseDemographicModel(Element e) Parses an element from an DOM document into a DemographicModel.Methods in pal.xml with parameters of type DemographicModelModifier and TypeMethodDescriptionstatic ElementElementFactory.createDemographicModelElement(DemographicModel demo, Document document) Creates an XML element representing a demographic model.